Retrieves a complete, stochastically-resolved phylogeny via the Fish Tree of Life API. If neither `species` nor `rank` are specified, returns the entire phylogeny.

fishtree_complete_phylogeny(species, rank,
  mc.cores = getOption("mc.cores", 1L))

Arguments

species

(Optionally) subset the results based on a vector of species names.

rank

(Optionally) subset the results based on the supplied taxonomic rank.

mc.cores

Number of cores to use in mclapply when subsetting the tree (default `1`)

Value

An object of class `"multiPhylo"`.

References

Rabosky, D. L., Chang, J., Title, P. O., Cowman, P. F., Sallan, L., Friedman, M., Kashner, K., Garilao, C., Near, T. J., Coll, M., Alfaro, M. E. (2018). An inverse latitudinal gradient in speciation rate for marine fishes. Nature, 559(7714), 392–395. doi:10.1038/s41586-018-0273-1

Enhanced polytomy resolution strengthens evidence for global gradient in speciation rate for marine fishes. https://fishtreeoflife.org/rabosky-et-al-2018-update/

Examples

if (FALSE) { tree <- fishtree_complete_phylogeny(rank = "Acanthuridae") sampled_tips <- fishtree_phylogeny(rank = "Acanthuridae")$tip.label all_tips <- tree[[1]]$tip.label new_tips <- setdiff(all_tips, sampled_tips) par(mfrow = c(2,2)) for (ii in 1:4) { plot(tree[[ii]], show.tip.label = FALSE, no.margin = TRUE) ape::tiplabels(pch = 19, col = ifelse(tree[[ii]]$tip.label %in% new_tips, "red", NA)) } }